Variant report

Variant	rs3789439
Chromosome Location	chr1:94579426-94579427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94573713..94576246-chr1:94579221..94581547,2	MCF-7	breast:
2	chr1:94571469..94574892-chr1:94577789..94583222,4	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874835	0.83[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11165076	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165079	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11165080	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11165082	0.85[ASN][1000 genomes]
rs11588391	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12025221	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035820	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17111122	0.82[TSI][hapmap]
rs1931564	0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1931566	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1931570	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789440	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789442	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789443	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789445	0.85[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs3827714	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147798	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147801	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147807	0.85[ASN][1000 genomes]
rs4147808	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61784007	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61784009	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1807674	chr1:94549175-94588191	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv870932	chr1:94579053-94607607	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv871679	chr1:94579426-94598568	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv871502	chr1:94579426-94607607	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv871306	chr1:94579426-94609478	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv871210	chr1:94579426-94629643	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789439	TMEM56	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94564600-94591800	Weak transcription	Right Atrium	heart
2	chr1:94567400-94585400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:94571000-94583000	Weak transcription	Pancreas	Pancrea
4	chr1:94571800-94581400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:94574600-94579800	Enhancers	Placenta	Placenta
6	chr1:94574600-94583000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:94575000-94579600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:94575800-94583000	Weak transcription	Left Ventricle	heart
9	chr1:94576400-94581800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:94576800-94582000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:94577000-94581200	Weak transcription	Liver	Liver
12	chr1:94577000-94581200	Weak transcription	Spleen	Spleen
13	chr1:94577200-94582000	Weak transcription	Lung	lung
14	chr1:94577400-94581400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:94577600-94581200	Enhancers	HepG2	liver
16	chr1:94577600-94582000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:94578400-94579600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:94578400-94579600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:94578400-94579800	Enhancers	Fetal Brain Male	brain
20	chr1:94578400-94581800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:94578600-94579800	Enhancers	Fetal Kidney	kidney
22	chr1:94578600-94580000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr1:94578800-94579600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:94578800-94579600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:94578800-94579800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr1:94578800-94580000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr1:94579000-94579600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:94579000-94579600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:94579000-94579600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:94579000-94579600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:94579000-94579800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:94579000-94579800	Enhancers	Fetal Muscle Leg	muscle
33	chr1:94579000-94580000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr1:94579000-94580000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:94579000-94580000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:94579200-94579600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr1:94579200-94579800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:94579200-94582400	Weak transcription	Fetal Heart	heart
39	chr1:94579400-94579600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:94579400-94579600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr1:94579400-94579600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:94579400-94579600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:94579400-94579600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr1:94579400-94579600	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:94579400-94579600	Enhancers	Fetal Thymus	thymus
46	chr1:94579400-94579600	Enhancers	Ovary	ovary
47	chr1:94579400-94579800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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